Python test_helper.get_reference函数代码示例

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本文整理汇总了Python中test_helper.get_reference函数的典型用法代码示例。如果您正苦于以下问题：Python get_reference函数的具体用法？Python get_reference怎么用？Python get_reference使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。

在下文中一共展示了get_reference函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。

示例1: testLeftNormalize

    def testLeftNormalize(self):
        #left normalize deletion
        norm_pos, norm_ref, norm_alts = left_normalize(get_reference(),'chr1',2,'CGCCG',['CG'])
        self.assertEqual(norm_pos,0)
        self.assertEqual(norm_ref,'AACGC')
        self.assertEqual(norm_alts[0],'AA')

        #left normalize insertion
        norm_pos, norm_ref, norm_alts = left_normalize(get_reference(),'chr4',12,'G',['GGG'])
        self.assertEqual(norm_pos,7)
        self.assertEqual(norm_ref,'C')
        self.assertEqual(norm_alts[0],'CGG')

开发者ID:a-wilson，项目名称:smash，代码行数:12，代码来源:normalize.py

示例2: testRectify2

    def testRectify2(self):
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       GC     G       20      PASS    .       GT      1/1\n
chr2   6   .       G      A       20      PASS    .       GT      1/1\n
"""
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       GCCG     GCA       20      PASS    .       GT      1/1\n
"""
        true_vars = vcf_to_ChromVariants(true_str,'chr2')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
        gtdict = _genotype_concordance_dict()
        cvs = ChromVariantStats(true_vars, pred_vars, [], [3,6], [3],gtdict)
        cvs.rectify(get_reference(),100)
        self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_OTH],1)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_OTH],1)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_OTH],0)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_OTH],0)
        self.assertEqual(cvs.num_pred[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],0)

开发者ID:amplab，项目名称:smash，代码行数:29，代码来源:eval_helper.py

示例3: testTruePosRectify

    def testTruePosRectify(self):
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4   3   .       TC     T       20      PASS    .       GT      1/1\n
chr4   5   .       TC     T       20      PASS    .       GT      1/1\n
chr4   8   .       C      T       20      PASS    .       GT      1/1\n
"""
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4   4   .       C     T       20      PASS    .       GT      1/1\n
chr4   5   .       TC    T       20      PASS    .       GT      1/1\n
chr4   7   .       TC    T       20      PASS    .       GT      1/1\n
"""
        true_vars = vcf_to_ChromVariants(true_str,'chr4')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr4')
        gtdict = _genotype_concordance_dict()
        cvs = ChromVariantStats(true_vars,pred_vars,[5],[4,7],[3,8],gtdict)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],1)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],1)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],1)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],1)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],1)
        cvs.rectify(get_reference(),100)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],1)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],2)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],0)

开发者ID:amplab，项目名称:smash，代码行数:32，代码来源:eval_helper.py

示例4: testRescueChromEvalVariants

    def testRescueChromEvalVariants(self):
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       GC     G       20      PASS    .       GT      1/1\n
chr2   6   .       G      A       20      PASS    .       GT      1/1\n
"""
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       GCCG     GCA       20      PASS    .       GT      1/1\n
"""
        true_vars = vcf_to_ChromVariants(true_str,'chr2')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_OTH],1)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_OTH],1)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_OTH],0)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_OTH],0)
        self.assertEqual(cvs.num_pred[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],0)
        self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],0)

开发者ID:amplab，项目名称:smash，代码行数:27，代码来源:eval_helper.py

示例5: testRectify

    def testRectify(self):
        # rectify CVS with a rescue-able indel
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   2   .       TGC     TAT       20      PASS    .       GT      1/1\n
"""
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       G     A       20      PASS    .       GT      1/1\n
chr2   4   .       C     T       20      PASS    .       GT      1/1\n
"""
        true_vars = vcf_to_ChromVariants(true_str,'chr2')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
        gtdict = _genotype_concordance_dict() # leave empty, we aren't testing this yet
        cvs = ChromVariantStats(true_vars,pred_vars,[],[3,4],[2],gtdict)
        # before rectify, no true positives
        self.assertTrue(all(map(lambda x: x == 0,cvs.num_tp.itervalues())))
        # one false negative indel
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_OTH],1)
        # two false positives SNPs
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],2)
        cvs.rectify(get_reference(),100)
        # after rectify, one true positive indel
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_OTH],1)
        # no false positives or false negatives
        self.assertTrue(all(map(lambda x: x == 0, cvs.num_fp.itervalues())))
        self.assertTrue(all(map(lambda x: x ==0, cvs.num_fn.itervalues())))

开发者ID:amplab，项目名称:smash，代码行数:29，代码来源:eval_helper.py

示例6: testChromEvaluateVariantsKnownFP

    def testChromEvaluateVariantsKnownFP(self):
        # one known true variant
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1    2       .       A       T       20      PASS     .      GT      0/1\n
        """
        # call var where known fp is, where true var is, where nothing is known
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1    2       .       A       T       20      PASS    .       GT      0/1\n
chr1    4       .       G       C       20      PASS    .       GT      1/1\n
chr1    7       .       G       A       20      PASS    .       GT      0/1\n
        """
        # known locations with NO variant
        known_fp_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1    1       .       A       T       20      PASS    .       GT       ./.\n
chr1    7       .       G       .       20      PASS    .       GT       0/0\n
        """
        true_vars = vcf_to_ChromVariants(true_str,'chr1')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
        known_fp_io = StringIO.StringIO(known_fp_str)
        known_fp = Variants(vcf.Reader(known_fp_io),MAX_INDEL_LEN,knownFP=True)
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50,known_fp.on_chrom('chr1'))
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],2) # usual definition, in pred vars but not in true
        self.assertEqual(cvs.calls_at_known_fp[VARIANT_TYPE.SNP],1) # call at location known to NOT have SNP

开发者ID:amplab，项目名称:smash，代码行数:29，代码来源:eval_helper.py

示例7: testGetSeq

    def testGetSeq(self):
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr3   2   .       TCGA     T       20      PASS    .       GT      1/1\n
chr3   9   .       A        AAAA    20      PASS    .       GT      0/1\n
"""
        variants = vcf_to_ChromVariants(pred_str,'chr3')
        window_tup = (1,13,'chr3')
        sequence = _get_seq(window_tup,variants.getAllVariants(),get_reference(),False)
        self.assertEqual(sequence[0],'ATTCGAAAATCG')
        self.assertEqual(sequence[1],'')
        sequence = _get_seq(window_tup,variants.getAllVariants(),get_reference(),True)
        self.assertEqual(sequence[0],'ATTCGATCG')
        self.assertEqual(sequence[1],'ATCGATCGAAAATCG')

开发者ID:ycaihua，项目名称:smash，代码行数:16，代码来源:rescue.py

示例8: testChromEvaluateVariantsSV

    def testChromEvaluateVariantsSV(self):
        #NB: SVs aren't rescued, just checked for within breakpoint tolerance
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1   6   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
"""
        #SV with exact position, exact allele match
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1   6   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
"""
        true_vars = vcf_to_ChromVariants(true_str,'chr1')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
        #SV with exact position, difference allele match
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1   6   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAATGC       20      PASS    .       GT      0/1
"""
        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
        #SV with position within tolerance, exact allele match
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1   4   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
"""

        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
        #SV outside of tolerance
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1   110   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
"""
        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],0)

开发者ID:amplab，项目名称:smash，代码行数:45，代码来源:eval_helper.py

示例9: testNBaseNormalization

    def testNBaseNormalization(self):
        vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4    2       .       A       ATCTT   20      PASS    .          GT      0/1\n
chr4    3       .       NN      N       20      PASS    .          GT      0/1\n
"""
        norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
        self.assertEqual(self.countRecords(norm_iter),1)

开发者ID:amplab，项目名称:smash，代码行数:9，代码来源:normalize.py

示例10: normalizeStringToWriter

 def normalizeStringToWriter(self,vcf_str):
     vcf_io = StringIO.StringIO(vcf_str)
     test_vcf = vcf.Reader(vcf_io)
     output_io = StringIO.StringIO()
     output_writer = VCFWriter('ref.fasta','name',output_io)
     map(lambda r: write(r,output_writer),normalize(get_reference(),test_vcf))
     outputStr = output_io.getvalue()
     outputStr = outputStr.replace('\n','\n\n')
     return vcf.Reader(StringIO.StringIO(outputStr))

开发者ID:a-wilson，项目名称:smash，代码行数:9，代码来源:normalize.py

示例11: testFullRescue

    def testFullRescue(self):
        fn_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   2   .       TGC     TAT       20      PASS    .       GT      1/1\n
"""
        fp_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       G     A       20      PASS    .       GT      1/1\n
chr2   4   .       C     T       20      PASS    .       GT      1/1\n
"""
        fn_vars = vcf_to_ChromVariants(fn_str,'chr2')
        fp_vars = vcf_to_ChromVariants(fp_str,'chr2')
        rescuer = SequenceRescuer('chr2',2,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
        self.assertTrue(rescuer.rescued)
        self.assertEqual(rescuer.windowsRescued,(0,0))

        fp_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       GC     G       20      PASS    .       GT      1/1\n
chr2   6   .       G      A       20      PASS    .       GT      1/1\n
"""
        fn_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       GCCG     GCA       20      PASS    .       GT      1/1\n
"""
        fp_vars = vcf_to_ChromVariants(fp_str,'chr2')
        fn_vars = vcf_to_ChromVariants(fn_str,'chr2')
        rescuer = SequenceRescuer('chr2',3,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
        self.assertTrue(rescuer.rescued)

        fn_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4   3   .       TC     T       20      PASS    .       GT      1/1\n
chr4   8   .       C      T       20      PASS    .       GT      1/1\n
"""
        fp_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4   4   .       C     T       20      PASS    .       GT      1/1\n
chr4   7   .       TC    T       20      PASS    .       GT      1/1\n
"""
        tp_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4   5   .       TC    T       20      PASS    .       GT      1/1\n
        """
        fn_vars = vcf_to_ChromVariants(fn_str,'chr4')
        fp_vars = vcf_to_ChromVariants(fp_str,'chr4')
        tp_vars = vcf_to_ChromVariants(tp_str,'chr4')
        rescuer = SequenceRescuer('chr4',3,fn_vars,fp_vars,tp_vars,get_reference(),50)
        self.assertTrue(rescuer.rescued)

开发者ID:ycaihua，项目名称:smash，代码行数:56，代码来源:rescue.py

示例12: testCollidingVariants

    def testCollidingVariants(self):
        vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1   5   .      A     TGC       20      PASS    .       GT      1/1\n
chr1   5   .      A      GGG       20      PASS     .      GT      1/1\n
"""
        norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
        count = self.countRecords(norm_iter)
        self.assertEqual(count,1)

开发者ID:a-wilson，项目名称:smash，代码行数:10，代码来源:normalize.py

示例13: testAggregate

    def testAggregate(self):
        # build two ChromVariantStats objects
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       G     A       20      PASS    .       GT      1/1\n
chr2   5   .       C     T       20      PASS    .       GT      1/1\n
"""
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2   3   .       G     A       20      PASS    .       GT      1/1\n
chr2   7   .       G     C       20      PASS    .       GT      1/1\n
"""
        true_vars = vcf_to_ChromVariants(true_str,'chr2')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
        gtdict = _genotype_concordance_dict() # leave empty for now
        cvs2 = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr3   3   .       G     A       20      PASS    .       GT      1/1\n
chr3   5   .       C     T       20      PASS    .       GT      1/1\n
"""
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr3   3   .       G     A       20      PASS    .       GT      1/1\n
chr3   4   .       T     A       20      PASS    .       GT      1/1\n
chr3   7   .       G     C       20      PASS    .       GT      1/1\n
"""
        true_vars = vcf_to_ChromVariants(true_str,'chr3')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr3')
        cvs3 = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        #cvs5 = ChromVariantStats(true_vars,pred_vars,[31],[49,79],[52],_genotype_concordance_dict())
        aggregator,errors = _aggregate([cvs2,cvs3])
        # test some sums
        self.assertEqual(cvs2.num_true[VARIANT_TYPE.SNP],2)
        self.assertEqual(cvs3.num_true[VARIANT_TYPE.SNP],2)
        self.assertEqual(aggregator(VARIANT_TYPE.SNP)['num_true'],4)
        self.assertEqual(cvs2.num_tp[VARIANT_TYPE.SNP],1)
        self.assertEqual(cvs3.num_tp[VARIANT_TYPE.SNP],1)
        self.assertEqual(aggregator(VARIANT_TYPE.SNP)['good_predictions'],2)

开发者ID:chapmanb，项目名称:smash，代码行数:43，代码来源:variants.py

示例14: testGenotypes

    def testGenotypes(self):
        # keep genotype info for a compound heterozygous call
        vcf_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1   2   .       A     C,T       20      PASS    .       GT      1/2\n
"""
        vcf = self.getVcf(vcf_str)
        record = normalize(get_reference(),vcf).next()
        self.assertEqual(record.samples[0].gt_nums, "1/2")

开发者ID:a-wilson，项目名称:smash，代码行数:11，代码来源:normalize.py

示例15: testChromEvaluateGenotypeConcordance

    def testChromEvaluateGenotypeConcordance(self):
        true_str = """##fileformat=VCFv4.0\n
        ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1    2       .       A       T       20      PASS     .      GT      0/1\n
chr1    5       .       C       T       20      PASS     .      GT      0/1\n
chr1    9       .       A       G       20      PASS     .      GT      1/1\n
        """
        pred_str = """##fileformat=VCFv4.0\n
        ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1    2       .       A       T       20      PASS     .      GT      1/1\n
chr1    6       .       C       G       20      PASS     .      GT      0/1\n
chr1    9       .       A       G       20      PASS     .      GT      1/1\n
        """
        true_vars = vcf_to_ChromVariants(true_str,'chr1')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HET][GENOTYPE_TYPE.HOM_VAR],1)
        self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][GENOTYPE_TYPE.HOM_VAR],1)
        # anything other than TP don't get counted in genotype concordance
        self.assertEqual(cvs._nrd_counts(VARIANT_TYPE.SNP),(1,2))
        # phased variants should be counted correctly
        true_str = """##fileformat=VCFv4.0\n
        ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1    2       .       A       T       20      PASS     .      GT      0|1\n
chr1    9       .       A       G       20      PASS     .      GT      1|1\n
        """
        pred_str = """##fileformat=VCFv4.0\n
        ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr1    2       .       A       T       20      PASS     .      GT      1|0\n
chr1    9       .       A       G       20      PASS     .      GT      1|1\n
        """
        true_vars = vcf_to_ChromVariants(true_str,'chr1')
        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HET][GENOTYPE_TYPE.HET],1)
        self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][GENOTYPE_TYPE.HOM_VAR],1)
        self.assertEqual(cvs._nrd_counts(VARIANT_TYPE.SNP),(0,2))

开发者ID:amplab，项目名称:smash，代码行数:41，代码来源:eval_helper.py

示例16: testCleanOnly

    def testCleanOnly(self):
        vcf_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2    6       .       g       cg       20      PASS    .       GT      0/1\n
"""
        norm = normalize(get_reference(),self.getVcf(vcf_str),50,True)
        record = norm.next()
        self.assertEqual(record.POS,6)
        self.assertEqual(record.REF,'G')
        self.assertEqual(record.ALT,['CG'])

开发者ID:a-wilson，项目名称:smash，代码行数:12，代码来源:normalize.py

示例17: testNormalizedToCollision

    def testNormalizedToCollision(self):
        vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2    4       .       C       T       20      PASS    .       GT      0/1\n
chr2    5       .       C       CGC     20      PASS    .       GT      0/1\n
chr4    2       .       A       AGG     20      PASS    .       GT      0/1\n
chr4    6       .       C       CTC     20      PASS    .       GT      0/1\n
"""
        norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
        r1 = norm_iter.next()
        r2 = norm_iter.next()
        r3 = norm_iter.next()
        r4 = norm_iter.next()
        self.assertEqual(r1.POS,4) # chr2 SNP doesn't change
        self.assertEqual(r2.POS,5) # chr2 insertion gets normed forward 1 base and slid back to original pos
        self.assertEqual(r2.REF,"C")
        self.assertEqual(r2.ALT,["CGC"])
        self.assertEqual(r3.POS,2)
        self.assertEqual(r3.REF,"A")
        self.assertEqual(r3.ALT,["AGG"])
        self.assertEqual(r4.POS,3)
        self.assertEqual(r4.REF,"T")
        self.assertEqual(r4.ALT,["TCT"])

        vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4    2       .       ATC     A     20      PASS    .       GT      0/1\n
chr4    6       .       CTC     C     20      PASS    .       GT      0/1\n
"""
        norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
        r1 = norm_iter.next()
        r2 = norm_iter.next()
        self.assertEqual(r1.POS,2)
        self.assertEqual(r1.REF,"ATC")
        self.assertEqual(r1.ALT,["A"])
        self.assertEqual(r2.POS,5)
        self.assertEqual(r2.REF,"TCT")
        self.assertEqual(r2.ALT,["T"])

开发者ID:a-wilson，项目名称:smash，代码行数:40，代码来源:normalize.py

示例18: testMultipleAltAlleles

    def testMultipleAltAlleles(self):
        # multiple alleles aren't normalized if the two alt alleles would be normalized differently
        vcf_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2    6       .       G       CG       20      PASS    .       GT      0/1\n
"""
        record = normalize(get_reference(),self.getVcf(vcf_str)).next()
        self.assertEqual(record.POS,3)
        self.assertEqual(record.REF,'G')
        self.assertEqual(record.ALT[0], 'GC')
        vcf_str2 = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr2    6       .       G       CG,C       20      PASS    .       GT      0/1\n
"""
        record = normalize(get_reference(),self.getVcf(vcf_str2)).next()
        self.assertEqual(record.POS,6)
        self.assertEqual(record.REF,'G')
        self.assertEqual(record.ALT[0],'CG')

开发者ID:a-wilson，项目名称:smash，代码行数:22，代码来源:normalize.py

示例19: testNormalizeTwoToCollision

    def testNormalizeTwoToCollision(self):
        vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr4    4       .       C       CTC     20      PASS    .       GT      0/1\n
chr4    6       .       C       CTC     20      PASS    .       GT      0/1\n
"""
        norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
        r1 = norm_iter.next()
        r2 = norm_iter.next()
        self.assertEqual(r1.POS,2)
        self.assertEqual(r1.REF,"A")
        self.assertEqual(r1.ALT,["ATC"])
        self.assertEqual(r2.POS,3)
        self.assertEqual(r2.REF,"T")
        self.assertEqual(r2.ALT,["TCT"])

开发者ID:a-wilson，项目名称:smash，代码行数:16，代码来源:normalize.py

示例20: testIndelDeletionMismatchedAllele

    def testIndelDeletionMismatchedAllele(self):
        true_str = """##fileformat=VCFv4.0\n
        ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr3   5        .       ATC     A       20      PASS    .       GT      0/1\n
        """
        pred_str = """##fileformat=VCFv4.0\n
        ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr3   5        .       ATCG    A       20      PASS    .       GT      0/1
        """
        true_vars = vcf_to_ChromVariants(true_str,'chr3')
        pred_vars = vcf_to_ChromVariants(pred_str, 'chr3')
        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
        self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],0)
        self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],1)
        self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],1)

开发者ID:amplab，项目名称:smash，代码行数:17，代码来源:eval_helper.py

注：本文中的test_helper.get_reference函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。

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Python test_helper.get_reference函数代码示例

示例1: testLeftNormalize

示例2: testRectify2

示例3: testTruePosRectify

示例4: testRescueChromEvalVariants

示例5: testRectify

示例6: testChromEvaluateVariantsKnownFP

示例7: testGetSeq

示例8: testChromEvaluateVariantsSV

示例9: testNBaseNormalization

示例10: normalizeStringToWriter

示例11: testFullRescue

示例12: testCollidingVariants

示例13: testAggregate

示例14: testGenotypes

示例15: testChromEvaluateGenotypeConcordance

示例16: testCleanOnly

示例17: testNormalizedToCollision

示例18: testMultipleAltAlleles

示例19: testNormalizeTwoToCollision

示例20: testIndelDeletionMismatchedAllele

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